Backbone-dependent rotamer library

Dunbrack R L Jr and M Karplus 1993. Backbone-dependent Rotamer Library for Proteins. Applic to Side-chain Prediction. Journal of Molecular Biology 230 543-574. 

MJ Bower, FE Cohen, RL Dunbrack Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library A new homology modeling tool. J Mol Biol 267 1268-1282, 1997. 

Analysis and prediction of side-chain conformation have long been predicated on statistical analysis of data from protein structures. Early rotamer libraries [91-93] ignored backbone conformation and instead gave the proportions of side-chain rotamers for each of the 18 amino acids with side-chain dihedral degrees of freedom. In recent years, it has become possible to take account of the effect of the backbone conformation on the distribution of side-chain rotamers [28,94-96]. McGregor et al. [94] and Schrauber et al. [97] produced rotamer libraries based on secondary structure. Dunbrack and Karplus [95] instead examined the variation in rotamer distributions as a function of the backbone dihedrals ( ) and V /, later providing conformational analysis to justify this choice [96]. Dunbrack and Cohen [28] extended the analysis of protein side-chain conformation by using Bayesian statistics to derive the full backbone-dependent rotamer libraries at all... 

MJ McGregor, SA Islam, MJE Sternberg. Analysis of the relationship between sidecham conformation and secondary stiaicture m globular proteins. J Mol Biol 198 295-310, 1987. RL Dunbrack Jr, M Karplus. Backbone-dependent rotamer library for proteins Application to sidecham prediction. J Mol Biol 230 543-571, 1993. 

Dunbrack, R.L., Jr. and Karplus, M. (1993) Backbone-dependent rotamer library for proteins. Application to side-chain prediction, J. Mol. Biol. 230, 543-574. 

Abbreviations used in table MC - Monte Carlo aa - amino acid vdW - van der Waals potential Ig - immunoglobulin or antibody CDR - complementarity-determining regions in antibodies RMS -root-mean-square deviation r-dependent dielectric - distance-dependent dielectric constant e - dielectric constant MD - molecular dynamics simulation self-loops - prediction of loops performed by removing loops from template structure and predicting their conformation with template sequence bbdep - backbone-dependent rotamer library SCMF - self-consistent mean field PDB - Protein Data Bank Jones-Thirup distances - interatomic distances of 3 Ca atoms on either side of loop to be modeled. 

SCWRL uses an alternative strategy, based on a probabilistic potential based on the backbone-dependent rotamer library. There are two terms the internal side-chain energy and the local side-chain-backbone interaction are modeled with an energy term proportional to —In prot where prot is the probability of the rotamer for the particular side-chain type and backbone conformation and a simple truncated linear steric term that models the repulsive interactions between atoms [93, 94]. 

The rotamer library used by SCWRL is backbone-dependent. Such libraries are considered to be more accurate than a backbone-independent rotamer library. A backbone-dependent rotamer library is more robust because the side-chain conformations are based on the protein s backbone dihedral angles ( and Both the secondary structure and the... 

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